Hi all, I'm trying to run tkregister2 and I have the following questions:
1. It seems to look for a talairach directory in the main subject directory. Does this mean I have to make/modify this directory each time i want the tkregister2 to manually correct the talairach transform?
2. when tkregister tries to initialize, it tries to read the talairach.xfm file, but it's not finding the talairach.xform. What does this mean? Here is the error output:
tkregister2 --mgz --s 000112_vc1552_test --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 0.874 -0.173 -0.004 -3.334; 0.188 0.957 -0.284 -10.880; 0.046 0.217 0.760 31.928; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/Users/Shared/freesurfer/subjects/00112_vc1552_test/mri/transforms/ talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /Users/Shared/freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /Users/Shared/freesurfer/subjects/talairach/mri/orig as 0
Thanks for any assistance!
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
Tracy Wang wrote:
Hi all, I'm trying to run tkregister2 and I have the following questions:
- It seems to look for a talairach directory in the main subject
directory. Does this mean I have to make/modify this directory each time i want the tkregister2 to manually correct the talairach transform?
It's looking for our talairach subject. I think this is part of the distribution, but if you don't have one, I've put a copy here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.tar.gz. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.tar.gz
- when tkregister tries to initialize, it tries to read the
talairach.xfm file, but it's not finding the talairach.xform. What
does this mean? Here is the error output:
It means that you did not run the initial talairaching stage (eg, recon-all -talairach). If you don't want to run this first, you can run tkregister2 with --regheader (but be careful to run subsequent calls to recon-all with -notalairach to keep from overwriting). Also note that you can get help with tkregister2 --help
doug
tkregister2 --mgz --s 000112_vc1552_test --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 0.874 -0.173 -0.004 -3.334; 0.188 0.957 -0.284 -10.880; 0.046 0.217 0.760 31.928; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/Users/Shared/freesurfer/subjects/00112_vc1552_test/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri corRead(): can't open file /Users/Shared/freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /Users/Shared/freesurfer/subjects/talairach/mri/orig as 0
Thanks for any assistance!
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, thanks for answering so quickly. Actually i ran recon-all -subjid 000112_vc1552_test -autorecon1 which i think would include the initial talairaching stage correct?
the talairach tranform seemed problematic both when viewed in tkmedit and the final objective funtion value in the mritotal.log (ours was 0.15870732).
does this mean that the talairaching failed at some place? How can i tell because mritotal seems to run to completion?
Thanks again, Tracy
On Jul 28, 2005, at 4:52 PM, Doug Greve wrote:
Tracy Wang wrote:Hi all,
I'm trying to run tkregister2 and I have the following questions:
- It seems to look for a talairach directory in the main subject
directory. Does this mean I have to make/modify this directory each time i want the tkregister2 to manually correct the talairach transform?
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ talairach.tar.gz.
It means that you did not run the initial talairaching stage (eg, recon-all -talairach). If you don't want to run this first, you can run tkregister2 with --regheader (but be careful to run subsequent calls to recon-all with -notalairach to keep from overwriting). Also note that you can get help with tkregister2 --help
doug
tkregister2 --mgz --s 000112_vc1552_test --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 0.874 -0.173 -0.004 -3.334; 0.188 0.957 -0.284 -10.880; 0.046 0.217 0.760 31.928; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/Users/Shared/freesurfer/subjects/00112_vc1552_test/mri/transforms/ talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /Users/Shared/freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /Users/Shared/freesurfer/subjects/talairach/mri/orig as 0
Thanks for any assistance!
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
Did it create the talairach.xfm file?
Tracy Wang wrote:
Hi Doug, thanks for answering so quickly. Actually i ran recon-all -subjid 000112_vc1552_test -autorecon1 which i think would include the initial talairaching stage correct?
the talairach tranform seemed problematic both when viewed in tkmedit and the final objective funtion value in the mritotal.log (ours was 0.15870732).
does this mean that the talairaching failed at some place? How can i tell because mritotal seems to run to completion?
Thanks again, Tracy
On Jul 28, 2005, at 4:52 PM, Doug Greve wrote:
Tracy Wang wrote:Hi all, I'm trying to run tkregister2 and I have the following questions: 1. It seems to look for a talairach directory in the main subject directory. Does this mean I have to make/modify this directory each time i want the tkregister2 to manually correct the talairach transform? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.tar.gz. It means that you did not run the initial talairaching stage (eg, recon-all -talairach). If you don't want to run this first, you can run tkregister2 with --regheader (but be careful to run subsequent calls to recon-all with -notalairach to keep from overwriting). Also note that you can get help with tkregister2 --help doug tkregister2 --mgz --s 000112_vc1552_test --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 0.874 -0.173 -0.004 -3.334; 0.188 0.957 -0.284 -10.880; 0.046 0.217 0.760 31.928; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/Users/Shared/freesurfer/subjects/00112_vc1552_test/mri/transforms/talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /Users/Shared/freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /Users/Shared/freesurfer/subjects/talairach/mri/orig as 0 Thanks for any assistance! Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
yes it did.
here's what's inside:
/Users/Shared/freesurfer/subjects/000112_vc1552_test/mri/transforms [cnlmac4:000112_vc1552_test/mri/transforms] twang% ls talairach.xfm [cnlmac4:000112_vc1552_test/mri/transforms] twang% more talairach.xfm MNI Transform File %Thu Jul 28 14:49:45 2005>>> /Users/Shared/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_1879/nu_8_dxyz.mnc /Users/Shared/freesurfer/lib/ mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.xfm -transformation /tmp/mritotal_1879/nu_8tmp2c.xfm -lsq9 -xcorr -model_mask /Us ers/Shared/freesurfer/lib/mni/bin/../share/mni_autoreg/ average_305_8_mask.mnc -center -3.474702 3.204924 -34.756481 -step 4 4 4 -tol 0.004 -simplex 2 %(Package MNI AutoReg, version 0.98r, compiled by nicks@storm.nmr.mgh.harvard.edu (powerpc-apple-darwin8.1.0) on 2005-06-23 at 13:55:39)
Transform_Type = Linear; Linear_Transform = 0.873943448066711 -0.172952562570572 -0.00371755170635879 -3.33402943611145 0.188183456659317 0.957016587257385 -0.284272521734238 -10.8803968429565 0.0461238026618958 0.216728016734123 0.760158002376556 31.9284954071045;
thanks, Tracy
On Jul 28, 2005, at 5:11 PM, Doug Greve wrote:
Did it create the talairach.xfm file?
Tracy Wang wrote:Hi Doug,
thanks for answering so quickly. Actually i ran recon-all -subjid 000112_vc1552_test -autorecon1 which i think would include the initial talairaching stage correct?
the talairach tranform seemed problematic both when viewed in tkmedit and the final objective funtion value in the mritotal.log (ours was 0.15870732).
does this mean that the talairaching failed at some place? How can i tell because mritotal seems to run to completion?
Thanks again, Tracy
On Jul 28, 2005, at 4:52 PM, Doug Greve wrote:
- It seems to look for a talairach directory in the main subject
directory. Does this mean I have to make/modify this directory each time i want the tkregister2 to manually correct the talairach transform?
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ talairach.tar.gz.
It means that you did not run the initial talairaching stage (eg, recon-all -talairach). If you don't want to run this first, you can run tkregister2 with --regheader (but be careful to run subsequent calls to recon-all with -notalairach to keep from overwriting). Also note that you can get help with tkregister2 --help
doug
tkregister2 --mgz --s 000112_vc1552_test --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 0.874 -0.173 -0.004 -3.334; 0.188 0.957 -0.284 -10.880; 0.046 0.217 0.760 31.928; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/Users/Shared/freesurfer/subjects/00112_vc1552_test/mri/ transforms/talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /Users/Shared/freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /Users/Shared/freesurfer/subjects/talairach/mri/orig as 0
Thanks for any assistance!
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
The final objective function seems too high, which indicates that mritotal wasn't able to find a good registration.
One approach worth trying is to do the skull-stripping first, then register the skull-stripped brain to the talairach space.
From my experience, it can correct the talairach registration problem in
most cases.
-Xiao
On Thu, 28 Jul 2005, Tracy Wang wrote:
Hi Doug, thanks for answering so quickly. Actually i ran recon-all -subjid 000112_vc1552_test -autorecon1 which i think would include the initial talairaching stage correct?
the talairach tranform seemed problematic both when viewed in tkmedit and the final objective funtion value in the mritotal.log (ours was 0.15870732).
does this mean that the talairaching failed at some place? How can i tell because mritotal seems to run to completion?
Thanks again, Tracy
On Jul 28, 2005, at 4:52 PM, Doug Greve wrote:
Tracy Wang wrote:Hi all,
I'm trying to run tkregister2 and I have the following questions:
- It seems to look for a talairach directory in the main subject
directory. Does this mean I have to make/modify this directory each time i want the tkregister2 to manually correct the talairach transform?
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ talairach.tar.gz.
It means that you did not run the initial talairaching stage (eg, recon-all -talairach). If you don't want to run this first, you can run tkregister2 with --regheader (but be careful to run subsequent calls to recon-all with -notalairach to keep from overwriting). Also note that you can get help with tkregister2 --help
doug
tkregister2 --mgz --s 000112_vc1552_test --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 0.874 -0.173 -0.004 -3.334; 0.188 0.957 -0.284 -10.880; 0.046 0.217 0.760 31.928; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/Users/Shared/freesurfer/subjects/00112_vc1552_test/mri/transforms/ talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /Users/Shared/freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /Users/Shared/freesurfer/subjects/talairach/mri/orig as 0
Thanks for any assistance!
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Tracy Wang -
Xiao Han